I am trying to build an amorphous model of polyurethane and water to simulate diffusion in LAMMPS. I have created a molecule of water and a single polyurethane molecule. How do I create an amorphous model with 100 polyurethane molecules and 50 water molecules. Which is the best way to save the file so that I can import that data file into LAMMPS ?
I need to run the simulation in NPT ensemble, unfortunately its not available in Avagadro. Any suggestions on how to do that ? I am trying to write the input file manually.